Methods for determining molecular pharmacology using label-free integrative pharmacology

Abstract

Disclosed are methods and machines to perform cluster analysis on label free biosensor data.

1 . A method of determining the similarity of a label-free biosensor data set comprising: a) obtaining a label free biosensor data set, b) performing a cluster analysis on said data set. 
     
     
         2 . The method of  claim 1 , wherein the cluster analysis comprises performing a Hierarchical clustering method. 
     
     
         3 . The method of  claim 2 , wherein the Hierarchical clustering method comprises an agglomerative method. 
     
     
         4 . The method of  claim 2 , wherein the Hierarchical clustering method comprises a divisive method. 
     
     
         5 . The method of  claim 4 , wherein the distance metric comprise a Euclidean distance method, squared Euclidean distance method, City-block distance method, Manhattan distance method, Pearson corrlation method, Pearson corrlation absolute value method, Uncentered correlation method, Centered correlation method, Spearman's rank correlation method, Kendall's tau method, maximum distance method, Mahalanobis distance method, or a cosine similarity method. 
     
     
         6 . The method of  claim 5 , wherein when the data set comprises data from a primary indice the distance metric comprises the uncentered correlation with absolute value. 
     
     
         7 . The method of  claim 6 , wherein when the data set comprises data from a molecule modulation indice the distance metric comprises either the uncentered correlation with absolute value method or the centered correlation with absolute value method. 
     
     
         8 . The method of  claim 1 , further comprising a distance matrix. 
     
     
         9 . The method of  claim 8 , further comprising a predefined clustering threshold, wherein the predefined clustering threshold is a biosensor parameter. 
     
     
         10 . The method of  claim 9 , further comprising a normalization or data pretreatment step. 
     
     
         11 . The method of  claim 10 , wherein the clustering analysis comprises a two-dimensional clustering analysis. 
     
     
         12 . The method of  claim 11 , further comprising the step of producing a heat map. 
     
     
         13 . The method of  claim 12 , wherein the method is a computer implemented method. 
     
     
         14 . The method of  claim 13 , further comprising the step of outputting results from the cluster analysis. 
     
     
         15 . A method of analyzing a label free biosensor data set comprising; receiving a label free biosensor data set record and performing a cluster analysis, wherein the record contains biosensor data measuring a biosensor response and outputting results from the cluster analysis, wherein the method is a computer implemented method. 
     
     
         16 . The method of  claim 15 , wherein receiving the label free biosensor data set record comprises receiving the label free biosensor data set record from a storage medium, wherein receiving the label free biosensor data set record comprises receiving the record from a computer system, wherein receiving the label free biosensor data set record comprises receiving the record from a biosensor system, wherein receiving the label free biosensor data set record comprises receiving the label free biosensor data set record via a computer network. 
     
     
         17 . One or more computer readable media storing program code that, upon execution by one or more computer systems, causes the computer systems to perform the method of  claim 15 . 
     
     
         18 . A computer program product comprising a computer usable memory adapted to be executed to implement the method of  claim 15 , wherein the computer program comprises a logic processing module, a configuration file processing module, a data organization module, and data display organization module, that are embodied upon a computer readable medium. 
     
     
         19 . A computer program product, comprising a computer usable medium having a computer readable program code embodied therein, said computer readable program code adapted to be executed to implement a method for generating the cluster analysis of  claim 15 , said method further comprising: providing a system, wherein the system comprises distinct software modules, and wherein the distinct software modules comprise a logic processing module, a configuration file processing module, a data organization module, and a data display organization module. 
     
     
         20 . A cluster analysis system, the system comprising: a data store capable of storing label free biosensor data set; a system processor comprising one or more processing elements, the one or more processing elements programmed or adapted to: receive the label free biosensor data set; store the label free biosensor data set in the data store; perform a cluster analysis on the label free biosensor data set; and output a result from the cluster analysis.